Input-file parser and commands

Files
file	command.h
	Provides the base class and various helpers for defining commands in the input file.
file	minimize.h
	Provides base class for defining the minimize commands.
file	ParamList.h
	Helper class for parsing command lines in input file.
file	parser.h
	Functions for parsing JDFTx input files.

Classes
class	Command
	Abstract base class for all commands. More...
class	DeprecatedCommand
	Base class for a deprecated command which will translate old syntax into the new command that replaces it. More...
struct	LinkDescription< Enum >
	Generate a description functor for addDescriptions() from an EnumStringMap. More...
struct	CommandMinimize
	Abstract base class for all the minimize commands. More...
class	ParamList
	Wrapper to std::istringstream that eases parsing of input file command lines. More...

Functions
std::map< string, Command * > &	getCommandMap ()
	Retrieve the map from command names to objects created during static initialization.
std::map< string, DeprecatedCommand * > &	getDeprecatedMap ()
	Retrieve the map from deprecated command names to objects.
template<typename GetDescription >
string	addDescriptions (string optionList, const GetDescription &getDescription, string spacer="\n+ ")
	Process the EnumStringMap::optionList() to add descriptions using an arbitrary functor. More...
string	nullDescription (const string &)
	Null description function that can be used with addDescriptions(). This can be useful for simply reformatting EnumStringMap::optionList()
template<typename Enum >
LinkDescription< Enum >	linkDescription (const EnumStringMap< Enum > &nameMap, const EnumStringMap< Enum > &descMap)
	Helper function to select appropriate LinkDescription<> by overloading. More...
std::shared_ptr< class SpeciesInfo >	findSpecies (string id, Everything &e, bool addSpecies=false)
	Find species matching an id (and create it from a wildcard if necessary) More...
bool	isReadable (string fname)
	Check if file is readable in an MPI friendly way. This function must be called from all processes, the file will be checked on one process and the result broadcast to all processes. More...
void	setAvailableFilename (string filenamePattern, string varName, string &target)
void	setAvailableFilenames (string filenamePattern, Everything &e)
	Apply setAvailableFilename for all standard input variables (action of CommandInitialState)
std::vector< std::pair< string, string > >	readInputFile (string filename)
	Read input from file into an array of command/argument-list pairs. This routine handles comments, line continuation as well as environment substitution. In MPI mode, the input will be read only on head and distributed to all the processes. More...
void	parse (std::vector< std::pair< string, string > > input, Everything &everything, bool printDefaults=false)
	Parse input and initialize everything. More...
void	printDefaultTemplate (Everything &e)
	Output command documentation in the form of an input file template. This will output the comments for all the commands, along with the default command line, if any. More...
void	writeCommandManual (Everything &e, string section)
	Output command docuemntation in Doxygen format which gets converted to the HTML and LaTeX manuals. More...

Detailed Description

Function Documentation

addDescriptions()

template<typename GetDescription >

string addDescriptions	(	string	optionList,
		const GetDescription &	getDescription,
		string	spacer = "\n+ "
	)

Process the EnumStringMap::optionList() to add descriptions using an arbitrary functor.

Template Parameters

GetDescription

Function/functor with the signature string GetDescription(const string&).

Parameters

optionList	List of strings separated by pipe characters as returned by EnumStringMap::optionList()
getDescription	A function/functor that returns the description given an option from optionList
spacer	Spacer to insert before each option/description pair

Returns

string containing the options along with their descriptions

findSpecies()

std::shared_ptr<class SpeciesInfo> findSpecies	(	string	id,
		Everything &	e,
		bool	addSpecies = false
	)

Find species matching an id (and create it from a wildcard if necessary)

Parameters

id	Psuedopotential species identifier string (typically chemical symbol)
e	Reference to Everything
addSpecies	Whether to add species from wildcards when trying to find id.

Returns

Smart pointer to SpeciesInfo corresponding to id.

isReadable()

bool isReadable

(

string

fname

)

Check if file is readable in an MPI friendly way. This function must be called from all processes, the file will be checked on one process and the result broadcast to all processes.

Parameters

fname

File name to check for

Returns

Whether file is readable

linkDescription()

template<typename Enum >

LinkDescription<Enum> linkDescription	(	const EnumStringMap< Enum > &	nameMap,
		const EnumStringMap< Enum > &	descMap
	)

Helper function to select appropriate LinkDescription<> by overloading.

Template Parameters

Enum	The template parameter of EnumStringMap

Parameters

nameMap	Link between enum members to corresponding name strings
descMap	Link between enum members to corresponding description strings

parse()

void parse	(	std::vector< std::pair< string, string > >	input,
		Everything &	everything,
		bool	printDefaults = false
	)

Parse input and initialize everything.

Parameters

input	List o commands and arguments as obtained by readInputFile()
everything	Reference to everything to initialize
printDefaults	If true, print status of commands that were invoked by default in addition to those invoked manually

printDefaultTemplate()

void printDefaultTemplate

(

Everything &

e

)

Output command documentation in the form of an input file template. This will output the comments for all the commands, along with the default command line, if any.

Parameters

e	A reference to Everything

readInputFile()

std::vector< std::pair<string,string> > readInputFile

(

string

filename

)

Read input from file into an array of command/argument-list pairs. This routine handles comments, line continuation as well as environment substitution. In MPI mode, the input will be read only on head and distributed to all the processes.

Parameters

filename

Name of file to read, or empty for reading from stdin

Returns

Pairs of commands and their argument lists

setAvailableFilename()

void setAvailableFilename	(	string	filenamePattern,
		string	varName,
		string &	target
	)

Set target to the filename for reading variable varName from file with pattern specified by filenamePattern if that file exists and is readable

writeCommandManual()

void writeCommandManual	(	Everything &	e,
		string	section
	)

Output command docuemntation in Doxygen format which gets converted to the HTML and LaTeX manuals.

Parameters

e	A reference to Everything
section	Which executable to generate documentation for i.e. only include commands whose section matches this